Download PDF MOLECULAR TO GLOBAL PHOTOSYNTHESIS by Mary D. Archer

Sinopsis

The word photosynthesis means ‘building up by light’, and the process is the building up, by plants, algae and certain bacteria under the action of sunlight, of organic compounds (mainly carbohydrates) from two very simple inorganic molecules, water (HzO) and carbon dioxide ((202). Put another way, photosynthesis is the light-driven reduction of atmospheric carbon dioxide by water to energy-rich organic compounds. But this reductionist, chemist’s view gives little hint of the central role of photosynthesis in sustaining life on Earth. Photosynthesis is the primary engine of the biosphere, essential to life since it is almost the sole process by which the chemical energy to maintain living organisms is made. It provides all our food, either directly in the form of green plants or indirectly in the form of animals that eat green plants or other animals that have eaten green plants. The only living organisms not sustained directly or indirectly by photosynthesis are the chemoautotrophs, primitive bacteria that harness the energy of inorganic compounds such as H2S to obtain the metabolic energy they need to grow and replicate, and the organisms that feed off them. Humans and other animals are heterotrophs-they ey cannot synthesise their own organic compounds from inorganic sources, but must ingest them as food. Photosynthetic organisms are photoautotrophs-able to harness solar energy to fix C02 (that is, store it in solid form as products of photosynthesis). Modern photosynthetic organisms come in a wide range of shapes and sizes, ranging from the 1-1Opn-1-sized photosynthetic bacteria and small, nonvascular mosses to giant sequoia trees that can reach more than 100 m in height.

Content

1. Photosynthesis and photoconversion
2. Light absorption and harvesting
3. Electron transfer in photosynthesis
4. Photosynthetic carbon assimilation
5. Regulation of photosynthesis in higher plants
6. The role of aquatic photosynthesis in solar energy conversion: a geoevolutionary perspective
7. Useful products from algal photosynthesis
8. Hydrogen production by photosynthetic microorganisms
9. Photoconversion and energy crops
10. The production of biofuels by thermal chemical processing of biomass
11. Photosynthesis and the global carbon cycle
12. Management of terrestrial vegetation to mitigate climate change
13. Biotechnology: its impact and future prospects

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Download PDF Molecular Biology and Bio technology Fourth Edition by John M. Walker and Ralph Rapley

Sinopsis

Microorganisms are capable of growing on a wide range of substrates and can produce a remarkable spectrum of products. The relatively recent advent of in vitro genetic manipulation has extended the range of products that may be produced by microorganisms and has provided new methods for increasing the yields of existing ones. The commercial exploitation of the biochemical diversity of microorganisms has resulted in the development of the fermentation industry and the techniques of genetic manipulation have given this well-established industry the opportunity to develop new processes and to improve existing ones. The term fermentation is derived from the Latin verb fervere, to boil, which describes the appearance of the action of yeast on extracts of fruit or malted grain during the production of alcoholic beverages. However, fermentation is interpreted differently by microbiologists and biochemists. To a microbiologist the word means any process for the production of a product by the mass culture of microorganisms. To a biochemist, however, the word means an energy-generating process in which organic compounds act as both electron donors and acceptors, that is, an anaerobic process where energy is produced without the participation of oxygen or other inorganic electron acceptors. In this chapter fermentation is used in its broader, microbiological context.

Content

1. Fermentation Technology
2. Molecular Analysis and Amplification Techniques
3. Recombinant DNA Technology
4. The Expression of Foreign DNA in Bacteria
5. Yeast Cloning and Biotechnology
6. Cloning Genes in Mammalian Cell-lines
7. Plant Biotechnology
8. Molecular, Structural and Chemical Biology in Pharmaceutical Research
9. Genetically Modified Foods
10. Molecular Diagnosis of Inherited Disease
11. DNA in Forensic Science
12. Vaccination and Gene Manipulation
13. Transgenesis
14. Protein Engineering
15. Bioinformatics
16. Immobilization of Biocatalysts
17. Downstream Processing: Protein Extraction and Purification
18. Monoclonal Antibodies
19. Biosensors

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Download PDF Single Molecule Alex E. Knight

Sinopsis

A new experimental paradigm, based on the detection of individual molecules, has been making great strides in the dissection of biomolecular function in vitro in the past two decades. A technological convergence – of improved detectors, probes, microfl uidics and other tools – is leading both to an explosion of this area of research and its development into a tool for investigating processes in living cells.

Imagine a busy motorway, packed with all kinds of vehicles. Now imagine that you are trying to describe the traffi c on that motorway (see Figure I.1 ). You could try to summarize it by a single number; the average speed of the traffi c would be a good example. This gives a good indication as to whether the traffi c is fl owing or obeying the speed limit, but it does not tell you much more. Sports cars may be tearing along in the outside lane, more cautious drivers cruising in the center lane, while trucks rumble along in the slow lane. Indeed, some vehicles may be pulled over on the hard shoulder. What’s more, vehicles will occasionally change lanes, slow down, or accelerate. We don’t get a full picture of this diversity from a single number, but this is the kind of measurement of molecular properties, quantities, or behavior that we usually make in the life sciences

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Download PDF Systems Biology METHODS IN MOLECULAR BIOLOGY™ by Ivan V. Maly

Sinopsis

What is systems biology? Over the past 40 years, practicing systems biologists delimited their field in a great number of ways. At times the definition was restricted to applications of the formal systems theory in biology; more recently, the tendency has been to focus on biomolecular interactions or on multivariate analysis as systems biology’s proper subject and method (1– 5) . This essay is written from a conservative biologist’s perspective and takes a less specific view of the topic. First, what should we call a system, in the context of the scientific way to parse the world into concepts? We recognize a system in a certain number of different and interacting objects. Noninteracting objects do not form a system. Also, it is hardly useful to see any substantial number of interacting, but identical objects as a system. Science has powerful methods to study aggregate behavior of identical objects. Notably, such methods tend to disregard the corpuscular nature of the individual objects and take a view of their collections as continua. In this case, biology can freely borrow methodologically from established areas of physics. In contrast, studying behavior of collections of interacting nonidentical objects remains a methodological challenge. We will, therefore, restrict the meaning of “system” to a system of interacting nonidentical parts. Study of a living object by discerning so-defined systems in it will then be called systems biology. Its status as a distinct discipline should engender no jealousy: The definition limits the subject of systems biology to what the scientific method is currently handling perhaps least confidently.

The difficulty appears to stem from the limitation of the human mind itself (6, 7) : we are nearly incapable of considering more than a few things at a time. Psychophysical experiments suggest the limit of about seven, which corresponds well to the number of the nonidentical, interacting elements that deserve to be called a system, as commonly perceived in the systems biology practice. It is important to observe that the limitation is not just to our intuition, but to rational reasoning as well. We can consider larger systems of course, but the effects resulting from interactions of more than a few elements at a time will likely be missed. To reason about systems whose complexity is beyond our immediate grasp, we must extend our mind with formal deduction, under the general rubric or mathematics. As applied to the natural world, it is termed mathematical modeling. Involving mathematics in nonsystems biological research can be necessitated by a desire of quantitative precision in understanding; in systems biology, it is indispensable for any progress whatsoever, because even the crudest qualitative effects are liable to be overlooked by the unaided mind that has evolved for rather different purposes.

That quantitative precision is rarely sought in modern systems biology is important to recognize, so as not to confuse the nature of the mathematics employed with the goals of the investigation. And certainly, those who are just considering employing systems analysis especially should not decide against it, if it is qualitative inference about their subject that they are after. We owe the quantitative, continuous-variable flavor of our most widely applied mathematics to its original development for the purposes of celestial mechanics and similarly particular problems of quantitative precision. As a consequence, the modern systemsbiological modeling has to be done most commonly in terms of dynamics of continuous quantities first, to an exceeding precision (“phosphorylation goes up by 73%”), and then the results are reinterpreted in terms of qualitative statements about discrete events (“this genotype permits cell division”), to arrive at the kind of knowledge that is actually being sought. This is no different from how experimental measurements are most commonly employed.

Content

1. Introduction: A Practical Guide to the Systems Approach in Biology
2. METHODS FOR ANALYZING BIOMOLECULAR SYSTEMS
3. Computational Modeling of Biochemical Networks Using COPASI
4. Flux Balance Analysis: Interrogating Genome-Scale Metabolic Networks
5. Modeling Molecular Regulatory Networks with JigCell and PET
6. Rule-Based Modeling of Biochemical Systems with BioNetGen
7. Ingeneue: A Software Tool to Simulate and Explore Genetic Regulatory Networks
8. SPATIAL ANALYSIS AND CONTROL OF CELLULAR PROCESSES
9. Microfluidics Technology for Systems Biology Research
10. Systems Approach to Therapeutics Design
11. Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models 
12. A Cell Architecture Modeling System Based on Quantitative Ultrastructural Characteristics 
13. Location Proteomics: Systematic Determination of Protein Subcellular Location
14. METHODS FOR LARGER-SCALE SYSTEMS ANALYSIS
15. Model-Based Global Analysis of Heterogeneous Experimental Data Using gfit
16. Multicell Simulations of Development and Disease Using the CompuCell3D Simulation Environment
17. BioLogic: A Mathematical Modeling Framework for Immunologists
18. Dynamic Knowledge Representation Using Agent-Based Modeling: Ontology Instantiation and Verification of Conceptual Models
19. Systems Biology of Microbial Communities

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Download PDF Molecular Biology of the Neuron (Molecular and Cellular Neurobiology) Second Edition by R. W. Davies

Sinopsis

The detailed study of neuronal function, in particular the function of neurons involved in complex processing and behavioural roles, requires several factors to be controlled, measured or exploited. Of relevance to the study of neuronal function are:

1. Drosophila: the short life cycle and simple culture conditions make it easy to control external environmental variables which are often more problematic in other species. In particular, the ‘sensory’ and ‘social’ interactions of the organism can easily be monitored and/or manipulated directly.
2. Behaviour: in order to unravel the neuronal pathways underlying behaviour, it is essential to study behaviours that can be assayed both qualitatively and quantitatively. There is a range of assays that have been developed over the years for both larval and adult stages of Drosophila. These include the use of visual, olfactory, tactile and auditory cues and assessment of responses with respect to reflex reactions as well as more complex learned behaviour.
3. Neurogenetics: Drosophila is one of the longest established genetic models with a formidable array of genetic and molecular tools that can be brought to bear upon any biological research area. This organism has given us valuable insights into the molecular, cellular and evolutionary bases of behaviour. In this chapter we will restrict our attention to those particularly relevant to neuroscience research in the organism.
4. Nervous system: the detailed neuronal architecture of the nervous system needs to be known in order for pathways involving multiple neurons to be investigated; i.e. neurons act as parts in circuits and context is critical. For Drosophila, traditional neuroanatomical techniques have produced gross maps of the nervous system through development and have also contributed valuable information about single neuronal projection patterns. The use of gene expression profiles (via enhancertraps) to unravel neuroanatomy was pioneered in Drosophila and recent techniques have refined such approaches to the extent that brain maps for Drosophila will soon be available to single neuron resolution.
5. Neurophysiology: sadly the small size of neurons in Drosophila makes traditional neurophysiology difficult. However, there have been advances recently with several emerging techniques that allow non-invasive recording of neuronal activity.
6. Neuroinformatics and high-throughput technologies, supporting informatics analysis toolkits and public database systems. Historically, Drosophila has had one of the most up-to-date and comprehensive databases describing the genetics of the organism (FlyBase: http://flybase.bio. indiana.edu) and this has been supplemented by a range of genome databases describing the sequences generated by the public and private genome sequencing projects and their annotation. In addition there are additional databases and resources of specific interest to Drosophila neuroscience that will be described towards the end of this chapter.

Drosophila melanogaster

Drosophila melanogaster (referred to here as Drosophila) is generally the first multicellular experimental organism that biologists are introduced to in their training. Unlike most other experimental systems in biology, their simple culture requirements are so simple and cost-effective that they can be maintained in high-school biology labs with ease. In a modern laboratory situation this makes getting started with Drosophila particularly easy, although as for any organism large-scale operations will require some dedicated equipment and support staff.
 

For the newcomer, there is a wealth of literature describing the culture requirements and the basic (and advanced) techniques possible. To begin with, we would recommend ‘Drosophila protocols’ (Sullivan et al. 2000), which is a laboratory manual (in format and weight). It describes in detail many of the common laboratory techniques including many of the recent molecular/transgenic manipulations used in Drosophila neuroscience, some of which we will describe in more detail here.

Content

1. Studying neuronal function using the Drosophila genetic system
2. Using mouse genetics to study neuronal development and function
3. Gene expression: from precursor to mature neuron
4. Protein trafficking in neurons
5. Ion channels and electrical activity
6. Molecular biology of transmitter release
7. Molecular biology of postsynaptic structures
8. Signal reception: Ligand-gated ion channel receptors
9. Signal reception: G protein-coupled receptors
10. Synapse-to-nucleus calcium signalling
11. Signalling by tyrosine phosphorylation in the nervous system
12. Mature neurons: Signal transduction-serine/ threonine kinases
13. The cytoskeleton
14. Neuronal Plasticity
15. Genetic basis of human neuronal diseases
16. Ageing and the death of neurones

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Download PDF Molecular Biology Techniques An intensive laboratory course by Walt Beam

Sinopsis

Molecular biology, in particular recombinant DNA research, has transformed research in the biological and medical sciences. This technology currently influences all aspects of biological research, has far-reaching applications in clinical diagnosis, and has led to important developments in agriculture and biotechnology. This course provides a hands-on introduction to molecular biological methods, including molecular cloning, polymerase chain reaction (PCR), Southern (DNA) blotting, Northern (RNA) blotting, DNA sequencing, oligonucleotide-directed mutagenesis, and protein expression, purification, and detection. You will work with a well-characterized gene (virD2) from the Agrobacterium tumefaciens tumor-inducing (Ti) plasmid. Virulence (v/r) genes mediate transfer of a specific region of the Ti plasmid from A. tumefaciens into host plant cells; oncogenes contained in the transferred DNA integrate into the host nuclear genome where their expression causes tumorous growth. Because we have studied virD2 previously, both starting materials and finished products for each experiment are available. All of the experiments you will do are "real," and most are published. This approach will demonstrate practical aspects of experimental design. Although the gene you will use is bacterial, the techniques apply to any research system.

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Download PDF Principles and Techniques of Biochemistry and Molecular Biology Seventh edition by KEITH WILSO

Sinopsis

Biochemistry involves the study of the chemical processes that occur in living organisms with the ultimate aim of understanding the nature of life in molecular terms. Biochemical studies rely on the availability of appropriate analytical techniques and on the application of these techniques to the advancement of knowledge of the nature of, and relationships between, biological molecules, especially proteins and nucleic acids, and cellular function. In recent years huge advances have been made in our understanding of gene structure and expression and in the application of techniques such as mass spectrometry to the study of protein structure and function. The Human Genome Project in particular has been the stimulus for major developments in our understanding of many human diseases especially cancer and for the identification of strategies that might be used to combat these diseases. The discipline of molecular biology overlaps with that of biochemistry and in many respects the aims of the two disciplines complement each other. Molecular biology is focussed on the molecular understanding of the processes of replication, transcription and translation of genetic material whereas biochemistry exploits the techniques and findings of molecular biology to advance our understanding of such cellular processes as cell signalling and apoptosis.

Content

1. Basic principles
2. Cell culture techniques
3. Centrifugation
4. Microscopy
5. Molecular biology, bioinformatics and basic techniques
6. Recombinant DNA and genetic analysis
7. Immunochemical techniques
8. Protein structure, purification, characterisation and function analysis
9. Mass spectrometric techniques
10. Electrophoretic techniques
11. Chromatographic techniques
12. Spectroscopic techniques: I Spectrophotometric techniques
13. Spectroscopic techniques: II Structure and interactions
14. Radioisotope techniques
15. Enzymes
16. Principles of clinical biochemistry
17. Cell membrane receptors and cell signalling
18. Drug discovery and development

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